Question

Log fold change from rlog

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2.1 years ago

Arindam Ghosh ▴ 530

How to calculate the logged fold-change from rlog values (obtatined from DESeq2)? I have a list of genes with rlog values in two conditions (no other information). Is lfc = rlog_A / rlog_B or fc = rlog_A - rlog_B?

logarithms R deseq • 969 views

ADD COMMENT • link updated 2.1 years ago by ATpoint 85k • written 2.1 years ago by Arindam Ghosh ▴ 530

score 2 · Answer 1 · 2022-10-21

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2.1 years ago

swbarnes2 14k

But note that DESeq doesn't use the rlog values when computing fold changes. The rlog values are just nice for some kinds of visualizations.

ADD COMMENT • link 2.1 years ago by swbarnes2 14k

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Yes, I am aware of that. In my situation I have only the rlog values only, unfortunately. How do I calculate the fold-change from this information?

ADD REPLY • link 2.1 years ago by Arindam Ghosh ▴ 530

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I would at least put them into limma then to get somewhat reliable stats rather than doing that by hand.

ADD REPLY • link 2.1 years ago by ATpoint 85k